My wild guess: He wanted to infiltrate the strongest enemy? or he wants Ran to be stronger then what he is.

I feel like he did it with a selfish reason, seeing as he would probably have killed Sei if not for Ran. Most likely he still cares for Ran (hopefully), but I don't think he betrayed because he wanted Ran to be stronger. My guess is that the other guy made him a deal of some sort, or a great benefit to receive if he goes to the other side.

Edit: After having read the entire manga, it was implied that Ran's brother wanted to dissuade Sei from becoming the head of the family and to experience the same "curse" that came with the line, so he joined enemy forces in order to protect those he cares about.

I just finished reading it. Still didn't get the reason why he betrayed them.

Spoiler (mouse over to view)

Especially because he seems to love Sei. It could be a possibility that he defected to the enemy because he wanted to disband the knight thingy but I don't think he'll go as far as trying to hurt Sei. And he hated Sei being the head of the family because she may get hurt

i think he wanted to break up the malicious cycle of the Otohri family, so he was trying to be "the bad guy"? Or he was trying to have it so Sei wasn't the head at least, because he didn't want her in such a dangerous position.